The present invention relates to a system for the direct sequencing of polymers such as DNA and RNA by passing the polymer through a nanoscale pore and measuring a light signal modulated by the polymer.
Genetic information is encoded in a molecule of deoxyribonucleic acid (DNA) as a sequence of nucleotides: guanine, adenine, thymine, and cytosine. Discovering the sequence of these nucleotides in DNA and other similar molecules is a foundational technology in biological studies.
One promising method of sequencing is “nanopore sequencing” in which a single strand of DNA, forming half of the DNA helix, is passed through a nanoscale opening in a membrane between two reservoirs. This nanopore opening may, for example, be a protein channel held in a lipid bilayer. An electrical potential or other gradient (i.e. molar concentrations. thermal, etc.) may be applied across the reservoirs to produce an ion flow between the reservoirs pulling the strand of DNA through the nanopore. As the strand passes through the nanopore, it modulates the ion current through the nanopore as a function of the size of the nucleotide obstructing the nanopore. This alteration in the ion current may then be analyzed to determine the nucleotide sequence. An example system of nanopore sequencing is described in PCT patent WO/2008102120 entitled: “Lipid Bilayer Sensor System”, and in European patent 2695949 entitled: “Nucleic Acid-based Nano Pores or Transmembrane Channels and their Uses”, both hereby incorporated by reference.
The electrical signals produced by changes in ion current through a nanopore with different nucleotides are very small in amplitude and accordingly long sampling times are required to distinguish the signals from noise, resulting in a slowing down of the sequencing process. The ability to obtain required sampling times may not be available because of the high speed of motion of the DNA strand through the nanopore.